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HomeAP 09258991 (superviser Kokhmetova А.)

AP 09258991 (superviser Kokhmetova А.)

Brief description of the project

(Project’s duration is 36 months, 2021-2023 г.)

  Project title: АРО9258991 «Mapping of quantitative trait loci associated with leaf rust resistance in wheat recombinant inbred lines population from Kazakhstan».

Leaf rust (Puccinia recondita Rob.et Desm f. Sp. tritici Eriks) causes serious damage to the crop and grain quality. Annual yield losses in Kazakhstan from leaf rust are from 10 to 30%, and in the years of epiphytoties – up to 50%. The use of genetically resistant varieties is the most efficient, economically and environmentally sound disease control method to reduce or eliminate the use of fungicides and minimize crop losses from rust. However, the population of rust pathogens overcomes the protection of resistant varieties, since virulent races of the pathogen appear, which affects the characteristics of interaction in the host – parasite system and complicates the breeding strategy. Identification of target genes and loci conferring disease resistance makes the process of developing and introducing wheat varieties more accurate and reliable. QTL mapping is a powerful tool for localizing genes on a chromosome region and identifying closely linked markers for marker-assisted selection. With the development of genetic maps, QTL mapping has become a widely used method for analyzing the quantitative genetic variation of a disease resistance trait. High density SNP gene chip technologies provide a valuable approach to QTL mapping due to fewer estimation errors, higher accuracy, higher density than SSR markers. Recent studies in Kazakhstan have shown that with the advent of new virulent races of the pathogen, many Lr genes have become ineffective. However, not enough studies have been carried out aimed at studying the genetic basis of quantitative resistance and identifying genomic regions associated with resistance to leaf rust in the breeding material of Kazakh wheat.

  The project idea. Although leaf rust (LR) Puccinia recondita is one of the most dangerous wheat diseases, no studies have been carried out to study the genetic basis of quantitative resistance and to identify genomic regions associated with LR resistance in Kazakhstan. Project is aimed at mapping QTL associated with LR resistance in Kazakhstani wheat recombinant inbred lines population.

  The Project goal: Mapping of quantitative trait loci associated with leaf rust resistance in wheat recombinant inbred lines population from Kazakhstan.

To achieve the goal the following steps will be carried out: the phenotyping of mapping population for seedling and adult plant resistance to LR; genotyping of RIL based on DArTseq™ sequencing technology using SNP markers; linkage map construction; identification of QTL and molecular markers associated with LR resistance.

  Expected research results: Expected results. Based on QTL mapping, genetic loci of quantitative traits QTL associated with resistance to wheat leaf rust will be identified and mapped, which will ultimately allow identifying the best combinations of alleles and wheat lines for use in wheat breeding for resistance to this disease. Genetic linkage maps will be constructed, QTL associated with seedling and adult plant resistance to leaf rust will be identified. Closely linked and associated with leaf rust resistance molecular markers, will be developed. Knowledge of the reaction of Kazakhstani breeding material to the prevailing races of the pathogen will be obtained, which will allow developing effective breeding strategies. The identified DNA markers will be used not only in practical breeding, but also in fundamental research aimed at understanding the nature of various types of resistance and isolation the underlying resistance genes.

  Scientific Supervisor of the project:

  Kokhmetova Alma, Doctor of Biological Sciences (Genetics), professor, corresponding member of the National Academy of Sciences RK, head of Genetics and Breeeding Laboratory, Institute of Plant Biology and Biotechnology (IPBB), National Coordinator European Biotechnology Association (EBTNA) for Kazakhstan.  Work experience is related to the study of disease resistance using Marker Assisted Selection (MAS) technology and associative mapping to improve the efficiency of the breeding for disease resistance. Since 2015 she was manager of 6 projects funded by Ministry of Education and Science and Ministry of Agriculture. Under her supervision 1 PhD, 4 PhD-doctoral, 12 master’s theses defended;1 PhD-dissertation is carried out. Hirsch Index is 7 (https://apps.webofknowledge.com/CitationReport.do?product=UA&search_mode=CitationReport&SID=E4M3qrpPTX4Xbgyu2tf&page=1&cr_pqid=6&viewType=summary). She has 300 publications, including 20 works in WOS/Scopus databases. WOS-ID: M-6618-2015; ORCHID-ID:0002-0186-7832.

  Research group:

Atishova M.N., higher education, master of pedagogical sciences, researcher of the laboratory of genetics and breeding since 2010. Experience: participated in 6 GF projects, conducted molecular/bioinformatic analyzes. Hirsch index 5. Published 49 works, including 11 in WOS/Scopus. She has undergone training on associative mapping of disease resistance of wheat, Institute of Cytology and Genetics SB RAS, Novosibirsk, RF (2019). Role in the project: Phenotyping and QTL mapping of leaf rust resistance. Scopus-ID: 55513476500; ORCHID-ID: 0000-0002-2270-571X.

 Keishilov Zh.S., higher education, master of agricultural sciences, junior researcher of IPPB since 2012. Experience: participated in 6 GF-projects. Hirsch index 1. Role in the project: Monitoring of pathogen in Kazakhstan regions, field evaluation of leaf rust resistance. Scopus-ID: 57221382183; ORCHID-ID: 0000-0003-2126-6951.

  Kumarbaeva M.T.,higher education, master of agricultural sciences, PhD doctoral student KazNAU, junior researcher, laboratory genetics and breeding, IPPB since 2014. Hirsch Index 2. Published 13 works, 2 in WOS/Scopus databases. Experience: executor of the GF-project, conducted a phytopathological assessment of promising wheat lines. Role in the project: Phenotyping of wheat samples for resistance to leaf rust pathotypes. Scopus-ID: 57213619570; ORCHID-ID: 0000-0002-5588-6772.

  Zhanuzak D.K., higher education, master of technical sciences, junior researcher at IPPB since 2012. Hirsch index 1. Fluent in phytopathological and molecular methods. Role in the project: Field evaluation of leaf rust resistance. Scopus-ID: 57226127734; ORCHID-ID: 0000-0002-2252-0870.

  Bolatbekova A.A., higher education, master of technical sciences, junior researcher laboratory assistant at IPPB since 2020. Hirsch index 1. Fluent in phytopathological and molecular methods. Role in the project: Field evaluation of leaf rust resistance. Scopus-ID: 57226105668; ORCHID-ID: 0000-0003-4694-9214.

  Malysheva A., bachelor, master student KazNU named after Al-Farabi, laboratory assistant, laboratory of genetics and breeding, IPPB. Hirsch index 1. Fluent in phytopathological and molecular methods. Role in the project: Field assessment and molecular screening of leaf rust resistance. Scopus-ID: 57226102193; ORCHID-ID: 0000-0002-9840-9570.

  Bakhytuly K., bachelor, master student KazNU named after Al-Farabi, laboratory assistant, laboratory of genetics and breeding, IPPB. Fluent in phytopathological and molecular methods. Role in the project: Field assessment and molecular screening of leaf rust resistance.

  Sehgal Deepmala, foreign project executor, PhD, Scientist, Plant Geneticist, Global Wheat Program, CIMMYT, Mexico. Member of Society of Genome India International, Member of Association for Promotion of DNA-Finger Printing and Associated DNA Technologies. Hirsch index 18 (Scopus ID 9638035500). Experience: allelic development of key candidate genes for resistance to abiotic and biotic stresses; assessment of genetic and functional diversity of plant varieties using GBS.

  List of publications of the project’s participants (2015-2021)

  1. Kokhmetova A., Madenova A., Kampitova G., Urazaliev R., Yessimbekova M., Morgounov A., Purnhauser L. 2016. Identification of leaf rust resistance genes in wheat cultivars produced in Kazakhstan//Cereal Research Communications.44(2):240–250.DOI:10.1556/0806.43.2015.056. If 0.708. WOS
  2. Kokhmetova A., Sehgal D., Ali S., Atishova M., Kumarbayeva M., Leonova I., Dreisigacker S. 2021. Genome-Wide Association Study of tan spot resistance in a hexaploid wheat collection from Kazakhstan. Front. Genet. 11:581214. DOI: 10.3389/fgene.2020.581214. IF 3.26. WOS Q2.
  3. A. Kokhmetova, O.Kremneva, G.Volkova, M.Atishova, Z.Sapakhova. 2017. Еvaluation of wheat cultivars growing in Kazakhstan and Russia for resistance to tan spot//Journal of Plant Pathology.99(1):161-167. DOI:10.4454/jpp.v99i1.3812.If 1.041. WOS, 2017г. Q3
  4. Morgounov A., Akin B., Demir L.Ã., Keser M., Kokhmetova A., Martynov S., Orhan Å., Ozdemir F., Ãzseven Ä., Sapakhova Z., Yessimbekova M. 2015.Yield gain in leaf rust resistant and susceptible winter wheat varieties due to fungicide application//Crop and Pasture Science.66(7):649-659.DOI:10.1071/CP14158. If 1.601. WOS Q2
  5. 5. Kokhmetova A., Sharma,R., Rsaliyev,S., Galymbek,K., Baymagambetova,K., Ziyaev,Z., Morgounov,A. 2018. Evaluation of Central Asian wheat germplasm for stripe rust resistance//Plant Genetic Resources.16(2):178-184.Doi:10.1017/S1479262117000132. IF792. WOS. Q4
  6. Кохметова А., Али С., Сапахова З., Атишова М.2018. Идентификация генотипов­носителей устойчивости к токсинам пиренофороза Ptr ToxA и Ptr ToxB Pyrenophora tritici-repentis в коллекции мягкой пшеницы//Вавиловский журнал генетики и селекции.
    22(8):978­-986. DOI:10.18699/VJ18.440. Scopus, SJR 0.15, Q4, 31-й процентиль.
  7. A. Kokhmetova, Atishova M., Kumarbayeva M., Leonova I.2019. Phytopathological screening and molecular marker analysis of wheat germplasm from Kazakhstan and CIMMYT for resistance to tan spot//Вавиловский журнал генетики и селекции.23(7):879-886. DOI:10.18699/VJ19.562. Scopus SJR 0.15, Q4, 31-й процентиль.
  8. Кохметова А.М., Коваленко Н.М., Кумарбаева М.Т. 2020. Структура популяции Pyrenophora tritici—repentis в Республике Казахстан и идентификация устойчивой к пиренофорозу гермоплазмы пшеницы. Вавиловский журнал генетики и селекции. 2020;24(7):722-729. DOI 10.18699/VJ20.666, SJR 0.15,Q4,31-й процентиль.
  9. Galymbek K., Kokhmetova A.M., Akan K., Madenova A.K., Atishova M.N.2017. Identification of germplasm of wheat on leaf rust (Puccinia recondita Rob.)//Ecology, Environment and Conservation.23(2):1211-1218. Scopus Q4,SJR 0.14.
  10. Madenova A.K., Kokhmetova A.M., Atishova M.N., Galymbek K., Yernazarova G.I.2019. Identification of carriers of resistance to common bunt (Tilletia caries) of winter wheat, Research on Crops.20(4):782-790.DOI:10.31830/2348-7542.2019.115. Scopus Q3, SJR 0.
  11. Madenova A.K., Kokhmetova A.M., Atishova M.N., Galymbek K., Keishilov Z.S. 2019.Molecular screening for resistance to common bunt (Tilletia caries) of wheat//Journal of Biotechnology. 305S:185. IF 2,667. Proc.‘European Biotechnology Congress 2019,Valencia,Spain,2019.
  12. Kokhmetova A., Atishova M.N. Identification wheat genotypes resistant to to tan spot Pyrenophora tritici-repentis//Bulletin of the NAS Republic of Kazakhstan.2:29-35.Doi:32014/2020.2518-1467.38
  13. Kokhmetova A., Atishova M.N., Galymbek K.2020.Identification of wheat germplasm resistant to leaf, stripe and stem rust using molecular markers//Bulletin of the NAS Republic of Kazakhstan.2:45-52.DOI:32014/2020.2518-1467.40
  14. Kokhmetova A, Rsaliyev S, Atishova M, Kumarbayeva M, Malysheva A, Keishilov Z, Zhanuzak D, Bolatbekova A. Evaluation of wheat germplasm for resistance to leaf rust (Puccinia triticina) and identification of the sources of Lrresistance genes using molecular markers // Plants. 2021; 10(7):1484. org/10.3390/plants10071484 БД Web of Science; Q1, IF 3.935, процентиль Scopus 56, процентиль JIF 80,21.
  15. Y. Kremneva, K.E. Gasiyan, A. V. Ponomarev, A.M.Kokhmetova, S. I. Novoseletsky. Influence of the tillage method on the development of leaf diseases of winter wheat // E3S Web Conf. Vol. 285, 2021. International Conference on Advances in Agrobusiness and Biotechnology Research (ABR 2021) DOI: 10.1051/e3sconf/202128502027 БД Scopus.

  Monographs, guidelines:

  1. Kokhmetova A.M. Genetic aspects of wheat adaptability. Almaty, 2005-225 p.
  2. Rsaliev Sh., Kokhmetova A.M., Sedlovsky A., Rsaliev A., Tileubaeva Zh.S., Tyupina L.N., Esenbekova G.T., Atishova M.N., Agabaeva A.Ch. Catalog of varieties and samples of wheat with genes for resistance to leaf rust: guidelines // Guidelines. — Almaty. 2011.- 100 p.
  3. Kokhmetova A.M., Sapakhova Z.B., Atishova M.N., Kumarbaeva M.T., Madenova A.K. Marker Assisted Selection for the devlopmant of advanced wheat lines resistant to yellow and leaf rust // Methodical recommendations. Almaty, 2015 — 32p.
  4. Kokhmetova A.M. Identification of sources of wheat resistance to tan spot. — Almaty. Same design. 2021.— 238 p.

  Patents, copyright certificates:

Four copyright certificates/patents for new wheat cultivars (Raminal, 2008; Alikhan,2014; Kazakhstan-75,2016; Stepnaya-53,2016), certificates for intellectual property (“Genotype-Environment” and “Genetic analysis» programs).

  Results obtained for 2021

The phenotyping of the Kazakh population of recombinant inbred wheat lines (RIL) Almaly / Anza for seedling and adult plant resistance to P. recondita was carried out. We selected 15 wheat lines that showed resistance to all 4 pathotypes of P. recondita simultaneously; among them 9 lines resistant to 3 pathotypes KHP/F, TKT/H, FKL/M, 19 lines resistant to pathotypes THT/F, TKT/H, FKL/M and 11 lines resistant to pathotypes THT/F, KHP/F, FKL/M were identified. The RIL population was phenotyped for adult plant resistance of P. recondita. The frequency of occurrence of resistant genotypes was 50.8% (104 genotypes), and those susceptible to leaf rust – 49.2% (101 genotypes). For the first time, 15 wheat lines that simultaneously showed resistance to 4 pathotypes of P. recondita and 7 RIL, which combined seedling and field resistance were identified; these 22 accessions are promising lines for breeding programs to improve leaf rust resistance. Based on the research results, 2 articles were published, including 1 article in the journal Plants, included in the Web of Science database (Q1, IF 3.935, Scopus percentile 56, JIF percentile 80.21) and 1 article included in the Scopus database (E3S Web Conf.).

  Research publications

 Articles in journals included in the Web of Science Core Collection database

  1. Kokhmetova A, Rsaliyev S, Atishova M, Kumarbayeva M, Malysheva A, Keishilov Z, Zhanuzak D, Bolatbekova A. Evaluation of wheat germplasm for resistance to leaf rust (Puccinia triticina) and identification of the sources of Lr resistance genes using molecular markers // Plants. 2021; 10(7):1484. DOI.org/10.3390/plants10071484 БД Web of Science; Q1, IF 3.935, процентиль Scopus 56, процентиль JIF 80,21.
  2. O. Y. Kremneva, K.E. Gasiyan, A. V. Ponomarev, A.M.Kokhmetova, S. I. Novoseletsky. Influence of the tillage method on the development of leaf diseases of winter wheat // E3S Web Conf. Vol. 285, 2021. International Conference on Advances in Agrobusiness and Biotechnology Research (ABR 2021) DOI: 10.1051/e3sconf/202128502027 БД Scopus.

  Results for 2022:

The isolation and cleaning of DNA of parental forms and RIL Almaly/Anza was carried out. DNA samples of 164 wheat genotypes were obtained, including 162 recombinant inbred wheat lines (RIL) Almaly/Anza combinations, as well as 2 parent forms (Almaly and Anza). Pure DNA samples with a ratio of 260/280 are selected more than 1.8 and with a ratio of 260/235 more than 2.2. After a quantitative assessment, DNA concentration was normalized up to 20 ng/µl for the subsequent conduct of PCR and genotyping. The genotyping of the RIL Almaly/Anza population, consisting of 162 recombinant inbred lines, using the new generation sequencing technology Dartseq ™ was done. The results of genotyping include 1969 polymorphic SNP markers located on 21 chromosomes, with an average number of SNP markers for a chromosome 93.76. The lengths of genetic maps for individual chromosomes ranged from 617 cm (chromosome 7D) to 132 cm (chromosome 4V). The largest number of markers was distributed among genomes A and B (40.98 and 40.83%, respectively), the smallest number of markers was represented in genome D (18.18%). The largest number of polymorphic markers was found on the 7D, 617 chromosomes, which amounted to 14.35%, then follow the 5D chromosomes (577; 19.23%) and 6D (540; 12%). The smallest number of markers was found on the 4V chromosome (132; 2.13%). Genome A contained 807 SNP markers, the average card density is 3.35 cm/marker, an average of 2.86 cm per locus. Genome B contained an 804 SNP marker with a card density 2.86 cm/marker and an average of 0.38 cm per locus. The D gene contained 358 SNP markers with a card density of 10.36 cm/marker and an average of 0.13 cm per locus. A field assessment of the age stability of the RIL Almaly/Anza population of wheat for resistance to P. Recondita was carried out. 88, 92, 104 and 89 lines, which showed high resistance in 2018, 2019, 2020 and 2022, respectively. Among the samples resistant to various races from 58 to 65% of the sample, stability in the field in 2022 also showed stability. Lines Ril Almaly/Anza 332-671, 335-674 and 445-788 were resistant in the field and to the races of TCTTR, TCPTQ and THTTR; lines 448-791, 451-794, 511-855, 513-857 and 514-859 – to the races THTQ, TCPTQ, THTTR; Line 526-872-to THTTQ, TCTTR, TCPTQ; Line 494-838-to ThTTQ, TCTTR, THTR. It was also noted that 5 RILs Almaly/Anza lines were characterized by group resistance to all four tested isolates to leaf rust. This is RILs Almaly/Anza-527-873; 495-839; 492-836; 361-700 and 358-697.

  Publications (2022):

Based on the results of 2022 studies, 4 articles were published, including 2 articles in publications recognized by CQAFSHE MSHE RK and 2 articles in collections of international conferences:

  1. Кеишилов Ж. С., Кохметова A.M., Кумарбаева M.T., Болатбекова A.A., Малышева A.A., Кохметова A.M. Жаздық бидайдың қоңыр тат (Puccinia recondita) ауруына солтүстік Қазақстанда жүргізілген мониторингі 2019-2021 // Вестник науки Казахского агротехнического университета им. С. Сейфуллина. – 2022. – №. 1(112). – Б. 930. DOI: 10.51452/kazatu.2022.1(112).930. КОКСОН
  2. Kokhmetova A., Malysheva A., Kumarbayeva M., Bolatbekova A., Kokhmetova A. 2022. Evaluation of the wheat recombinant inbred lines for resistance to leaf rust // Научный журнал Доклады НАН РК, (2), 48–60. DOI: 10.32014/2022.2518-1483.147. КОКСОН.
  3. Болатбекова А.А., Кохметова А.М. Идентификация носителей пшенично-ржаной транслокации 1BS/1R с помощью молекулярных маркеров // Сборник Международной научной конференции «Становление и развитие экспериментальной биологии в Таджикистане», посвященная 90-летию со дня рождения академика Ю.С. Насырова. – Душанбе, 2022. – С. 173-175.
  4. Кохметова А.М., Уразалиев Р.А., Рсалиев Ш.С., Кеишилов Ж.С., Кумарбаева М.Т., Мухаметжанов К.С., Бахытулы К. Использование гермоплазмы диких сородичей для повышения устойчивости к болезням пшеницы // Сборник конференции «Интродукция, сохранение биоразнообразия и зеленое строительство в условиях изменяющегося климата и антропогенного воздействия. г. Актау. – 2022. – С. 86-89.